diff --git a/.github/workflows/links-internal.yml b/.github/workflows/links-internal.yml index e19a377bf6..25eeaea752 100644 --- a/.github/workflows/links-internal.yml +++ b/.github/workflows/links-internal.yml @@ -18,7 +18,7 @@ jobs: - name: Get yarn cache directory path id: yarn-cache-dir-path run: echo "::set-output name=dir::$(yarn cache dir)" - - uses: actions/cache@v1 + - uses: actions/cache@v4 id: yarn-cache with: path: ${{ steps.yarn-cache-dir-path.outputs.dir }} diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index 7ba35cc531..2b25561c8f 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -12,7 +12,7 @@ jobs: - name: Get yarn cache directory path id: yarn-cache-dir-path run: echo "::set-output name=dir::$(yarn cache dir)" - - uses: actions/cache@v1 + - uses: actions/cache@v4 id: yarn-cache # use this to check for `cache-hit` (`steps.yarn-cache.outputs.cache-hit != 'true'`) with: path: ${{ steps.yarn-cache-dir-path.outputs.dir }} diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index e3d4f71ffa..abcc3a6eb3 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -27,7 +27,7 @@ jobs: run: echo "dir=$(yarn cache dir)" >> $GITHUB_OUTPUT - name: Cache Yarn Dependencies - uses: actions/cache@v3 + uses: actions/cache@v4 id: yarn-cache with: path: ${{ steps.yarn-cache-dir-path.outputs.dir }} diff --git a/config.json b/config.json index ebe2717c3c..4ac1f28278 100644 --- a/config.json +++ b/config.json @@ -83,7 +83,7 @@ "name": "GenOuest" }, "elixir-it": { - "name": "ELIXIR-IT/Laniakea" + "name": "ELIXIR-IT" }, "ifb": { "name": "ELIXIR-FR/IFB" diff --git a/content/community/governance/gcb/index.md b/content/community/governance/gcb/index.md index 2c0301c370..85773e6dc0 100644 --- a/content/community/governance/gcb/index.md +++ b/content/community/governance/gcb/index.md @@ -33,18 +33,24 @@ You can learn more about **SIGs** in our dedicated tutorials below, or explore o
-
-
-
+
+
+ - @@ -68,6 +74,10 @@ from GEB and from GTB to be also members of the GCB. Therefore, it is recommende SIG members, and especially the representatives, are encouraged to join WG meetings or talk to WG representatives to raise issues or request help. For example, SIG members could request assistance from the tools and workflows WG. WGs might contact SIGs to collect feedback from the community. +## Meetings Calendar + + + ## Origins During GCC 2023, we discussed how to empower the Galaxy community in terms of project planning, decision-making, execution, and overall governance. The Galaxy Community Board (GCB) was formed to take over from the Global Galaxy Steering Committee. @@ -79,4 +89,4 @@ This page is brought to you by: with thanks for editing and review from: - [Saskia Hiltemann](https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/) - - [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/) \ No newline at end of file + - [Helena Rasche](https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/) diff --git a/content/community/governance/geb/index.md b/content/community/governance/geb/index.md index ed90f1ce1f..7bab5d978d 100644 --- a/content/community/governance/geb/index.md +++ b/content/community/governance/geb/index.md @@ -174,5 +174,6 @@ The GEB is a group of Galaxy advocates from around the world. It is currently (2 * [Australian BioCommons](https://www.biocommons.org.au/), [The University of Queensland](https://www.uq.edu.au/), Australia * **[Bérénice Batut](https://research.bebatut.fr)** * [Institut Francais de Bioinformatique]([https://www.open.ac.uk/research/faculties](https://www.france-bioinformatique.fr/)), [AuBi](https://mesocentre.uca.fr/projets-associes/plateforme-aubi), France - +* **[Saskia Hiltemann](https://www.linkedin.com/in/shiltemann/)** + * [University of Freiburg](https://uni-freiburg.de/), Germany & The Netherlands * But, well, obviously not. Thank you Ross. diff --git a/content/community/sig/index.md b/content/community/sig/index.md index aff4c09343..7e2a27ad44 100644 --- a/content/community/sig/index.md +++ b/content/community/sig/index.md @@ -7,12 +7,18 @@ autotoc: false Active Galaxy communities are encouraged to participate in (or form) their own SIG, with a focus on specific shared interests. You can learn more in our dedicated tutorial: [What's a SIG?](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_define/tutorial.html) -In the following you will find a list of current active Special Interest Groups. If you can't find yourself in this list we always welcome new SIGs. -You can read more about the [GCB and SIGs](/community/governance/gcb/) or learn [how to set up your own](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_create/tutorial.html). +# Galaxy Communities Calendar +Check out the upcoming meetings across the communities. + + +*Please note: The Galaxy Community Board introduced this in December 2024, so we are still collecting communities to add to it! Do you not see your community? [Follow this FAQ](https://training.galaxyproject.org/training-material/topics/community/faqs/community_activites_calendar.html) to add it!* # Directory of Special Interest Groups +In the following you will find a list of current active Special Interest Groups. If you can't find yourself in this list we always welcome new SIGs. +You can read more about the [GCB and SIGs](/community/governance/gcb/) or learn [how to set up your own](https://training.galaxyproject.org/training-material/topics/community/tutorials/sig_create/tutorial.html). + --- ## Communities of Practice diff --git a/content/community/sig/singlecell/index.md b/content/community/sig/singlecell/index.md index 53e75d7c6a..26b3ea503c 100644 --- a/content/community/sig/singlecell/index.md +++ b/content/community/sig/singlecell/index.md @@ -68,14 +68,9 @@ Our meeting agenda is: # How can you join & other important links -Start by joining our [🖖🏾SPOC Chatroom](https://matrix.to/#/#spoc3:matrix.org) and introduce yourself! (Or you can just lurk there for a bit!) - - -    [Mailing list](https://lists.galaxyproject.org/lists/single-cell-cop.lists.galaxyproject.org/) - -    [ClickUp site](https://sharing.clickup.com/9015477668/b/h/5-90152810734-2/557452707486fef) & [Sign-up to edit](https://forms.gle/TgCyHMiBcwFBskef6) - -    [🖖🏾SPOC Google Calendar](https://calendar.google.com/calendar/embed?src=galaxy.sc.cop%40gmail.com&ctz=Europe%2FLondon) - -    [🖖🏾SPOC iCalendar for non-google users](https://calendar.google.com/calendar/ical/galaxy.sc.cop%40gmail.com/public/basic.ics) - -    [Meeting Notes doc](https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtfmHSA/edit?usp=sharing) <--- There's a section here called 'New here?' that gives tips on how to start contributing as well! - -    [User Matrix Channel](https://matrix.to/#/#Galaxy-Training-Network_galaxy-single-cell:gitter.im) +1. Start by joining our [🖖🏾SPOC Chatroom](https://matrix.to/#/#spoc3:matrix.org) and introduce yourself! (Or you can just lurk there for a bit!) + +2. Then, follow the instructions on our ['👋🏾New here?'](https://docs.google.com/document/d/19W--oeFoEgfZbw9MWvky_A__554th-VG3ryOqtfmHSA/edit?tab=t.34ufduimwwz5) tab for key links to calendars, notes, how to contribute, and more! ## Key words diff --git a/content/elixir-it/cite/index.md b/content/elixir-it/cite/index.md new file mode 100644 index 0000000000..fbc2cc71da --- /dev/null +++ b/content/elixir-it/cite/index.md @@ -0,0 +1,61 @@ +--- +title: Cite us +--- + +

If UseGalaxy.it and/or Laniakea helped you, please do not forget to cite us.

+
+ +

Publications

+ +
+ +

2024

+
    + +
  1. Tangaro,M.A. et al. (2024) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. NAR Genomics and Bioinformatics, 2024, 6(4), lqae140. DOI: 10.1093/nargab/lqae140.
    2. +
    +
  2. The Galaxy Community (2024) The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Nucleic Acids Research, 2024, 52(W1), pp. W83–W94. DOI: 10.1093/nar/gkae410.
    3. +
+ + +

2023

+
    +
  1. Tangaro,M.A. et al. (2023) The Laniakea Dashboard and Storage Encryption Components: A Foundation for Developing On-Demand Cloud Services for Life Science. Communications in Computer and Information Science, 2023, 1668 CCIS, pp. 179–191. DOI: 10.1007/978-3-031-25380-5_14.
    2. +
    +
  2. Mandreoli,P. et al. (2023) Using “Galaxy-rCASC”: A Public Galaxy Instance for Single-Cell RNA-Seq Data Analysis. Methods in Molecular Biology, 2023, 2584, pp. 311–335. DOI: 10.1007/978-1-0716-2756-3_16.
    3. +
+ + +

2022

+
    +
  1. The Galaxy Community (2024) The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Nucleic Acids Research, 2022, 50(W1), pp. W345–W351. DOI: 10.1093/nar/gkac247.
    2. +
+ + +

2021

+
    +
  1. Tangaro,M.A. et al. (2021) Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinformatics, 2021, 22, 544. DOI: 10.1186/s12859-021-04401-3.
    2. +
    +
  2. Zambelli,F. et al. (2021) aScan: A Novel Method for the Study of Allele Specific Expression in Single Individuals. Journal of Molecular Biology, 2021, 433(11), 166829. DOI: 10.1016/j.jmb.2021.166829.
    3. + +
+ + +

2020

+
    +
  1. Chiara,M. et al. (2020) VINYL: Variant prIoritizatioN by survivaL analysis. Bioinformatics, 2020, 36(24), pp. 5590–5599. DOI: 10.1093/bioinformatics/btaa1067.
    2. +
    +
  2. Chiara,M. et al. (2020) CorGAT: A tool for the functional annotation of SARS-CoV-2 genomes. Bioinformatics, 2020, 36(22-23), pp. 5522–5523. DOI: 10.1093/bioinformatics/btaa1047.
    3. +
    +
  3. Castrignanò,T. et al. (2020) ELIXIR-IT HPC@CINECA: High performance computing resources for the bioinformatics community. BMC Bioinformatics, 2020, 21, 352. DOI: 10.1186/s12859-020-03565-8.
    4. +
    +
  4. Tangaro,M.A. et al. (2020) Laniakea: an open solution to provide Galaxy “on-demand” instances over heterogeneous cloud infrastructures. GigaScience, 2020, 9(4), giaa033. DOI: 10.1093/gigascience/giaa033.
    5. +
+ + +

2019

+
    +
  1. Zanardi,N. et al. (2019) PIPE-T: a new Galaxy tool for the analysis of RT-qPCR expression data. Scientific Reports, 2019, 9(1), 17550. DOI: 10.1038/s41598-019-53155-9.
    2. +
+
+ diff --git a/content/elixir-it/events/archive/main.md b/content/elixir-it/events/archive/main.md index fbb3550448..1bd0646e21 100644 --- a/content/elixir-it/events/archive/main.md +++ b/content/elixir-it/events/archive/main.md @@ -1,6 +1,6 @@ --- -title: ELIXIR-IT/Laniakea Galaxy Event Archive +title: Galaxy Italy Event Archive --- -Old events relevant to the ELIXIR-IT/Laniakea Galaxy community. +Old events relevant to the Italian Galaxy community. diff --git a/content/elixir-it/events/main.md b/content/elixir-it/events/main.md index dc4f1522dc..5ca3eff538 100644 --- a/content/elixir-it/events/main.md +++ b/content/elixir-it/events/main.md @@ -1,10 +1,10 @@ --- -title: ELIXIR-IT/Laniakea Event Horizon +title: Galaxy Italy Event Horizon --- events -Upcoming (and past) events with content relevant to the ELIXIR-IT/Laniakea Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/). +Upcoming (and past) events with content relevant to the Italian Galaxy community. For events prior to this year, see the [events archive](/elixir-it/events/archive/). ### Advertise your event! diff --git a/content/elixir-it/lead.md b/content/elixir-it/lead.md.off similarity index 100% rename from content/elixir-it/lead.md rename to content/elixir-it/lead.md.off diff --git a/content/elixir-it/lead1.md b/content/elixir-it/lead1.md new file mode 100644 index 0000000000..12643926b9 --- /dev/null +++ b/content/elixir-it/lead1.md @@ -0,0 +1,8 @@ +
+ +
+ +[![](/images/logos/usegalaxy-it.png)](https://usegalaxy.it) + +
+
diff --git a/content/elixir-it/lead2.md b/content/elixir-it/lead2.md new file mode 100644 index 0000000000..e9eb9b8dc5 --- /dev/null +++ b/content/elixir-it/lead2.md @@ -0,0 +1,3 @@ +**Galaxy** is a user-friendly open-source web platform designed to facilitate accessible, reproducible, and transparent computational research. It provides access to a vast collection of free-to-use, well-documented and maintained tools. + +**Galaxy Italy** provides Elixir Italy users and beyond compute and storage resources for running several tools in different research domains. For more information, issues and suggestions please contact us by mail. diff --git a/content/elixir-it/lower.md b/content/elixir-it/lower.md new file mode 100644 index 0000000000..ed97d539c0 --- /dev/null +++ b/content/elixir-it/lower.md @@ -0,0 +1 @@ +--- diff --git a/content/elixir-it/lower1.md b/content/elixir-it/lower1.md.off similarity index 100% rename from content/elixir-it/lower1.md rename to content/elixir-it/lower1.md.off diff --git a/content/elixir-it/lower2.md b/content/elixir-it/lower2.md.off similarity index 100% rename from content/elixir-it/lower2.md rename to content/elixir-it/lower2.md.off diff --git a/content/elixir-it/main1.md b/content/elixir-it/main1.md new file mode 100644 index 0000000000..fb2fa346db --- /dev/null +++ b/content/elixir-it/main1.md @@ -0,0 +1,11 @@ +--- +title: Galaxy Italy +subtitle: The homepage of the Italian Galaxy community +--- +
+
+

The Italian Galaxy server

+

The Italian Galaxy server UseGalaxy.it is maintained primarily by ELIXIR-ITALY, in collaboration with many academic groups across Italy. Please check our Terms of Use before using the server.

+

The following Institutions are actively providing resource to usegalaxy.it: CNR, INFN, University of Bari, Consortium GARR, CINECA and University of Milan.

+
+
diff --git a/content/elixir-it/main2.md b/content/elixir-it/main2.md new file mode 100644 index 0000000000..f96fd648af --- /dev/null +++ b/content/elixir-it/main2.md @@ -0,0 +1,67 @@ +--- +title: Galaxy Italy +subtitle: The homepage of the Italian Galaxy community +--- + + + + +
+
+
+

Contact

+

Ask for help, tools, or temporary increase of quota on our support forum

+
+ qsupport +



+ Contact support +
+
+
+
+
+

Get information

+

Be updated on the Italian Galaxy community activities! Subscribe to our mailing list.

+
+ training +


+ Newsletter +
+
+
+
+
+

Laniakea

+

Need to deploy your own Galaxy instance? Have a look to Laniakea.

+
+ Laniakea +



+ Get access +
+
+
+
+
+

Citation

+

Have you used the Italian Galaxy server or Laniakea for your data analysis?

+
+
+ citation +


+ Cite us! +
+
+
+
+
+

Elixir Italy

+

For any questions regarding ELIXIR-Italy initiatives, please contact us.

+

+
+ team +

+ Web site +
+
+
+
diff --git a/content/elixir-it/main3.md b/content/elixir-it/main3.md new file mode 100644 index 0000000000..8ee3e15b18 --- /dev/null +++ b/content/elixir-it/main3.md @@ -0,0 +1,29 @@ +--- +title: Galaxy Italy +subtitle: Data policy +--- + +# Our Data Policy + + + + + + + + + + +
Registered UsersUnregistered UsersGDPR Compliance
User data on UseGalaxy.it (i.e. datasets, histories) will be available as long as they are not deleted by the user. + Once marked as deleted the datasets will be permanently removed within 14 days. If the user "purges" the dataset in the + Galaxy, it will be removed immediately, permanently. + In special cases, an extended quota can be requested + for a limited time period.. + Processed data will only be accessible during one browser session, using a + cookie to identify your data. This cookie is not used for any other purposes + (e.g. tracking or analytics). + If UseGalaxy.it service is not accessed for 90 days, those datasets will be + permanently deleted. + The Galaxy service complies with the EU General Data Protection Regulation + (GDPR). You can read more about this on our + Terms and Conditions.
diff --git a/content/elixir-it/main.md b/content/elixir-it/main4.md similarity index 70% rename from content/elixir-it/main.md rename to content/elixir-it/main4.md index 540748841e..4cd483b9e5 100644 --- a/content/elixir-it/main.md +++ b/content/elixir-it/main4.md @@ -1,13 +1,18 @@ --- -title: Laniakea@ReCaS +title: Galaxy Italy +subtitle: Laniakea on-demand platform --- +# Laniakea@ReCaS +
-The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks. +The **Laniakea@ReCaS** service, based on Laniakea software stack, provides the possibility to automate the creation of Galaxy-based virtualized environments through an easy setup procedure, providing an on-demand workspace ready to be used by life scientists and bioinformaticians. At the end of the configuration process, the user gains access to a private, production-grade, fully customizable, Galaxy virtual instance. Laniakea features the deployment of a stand-alone or cluster-backed Galaxy instances, shared reference data volumes, encrypted data volumes and rapid development of novel Galaxy flavours for specific tasks. + +For more information about Laniakea, please subscribe to our mailing list. -[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-secondary .trim-p} +[Get Access](https://laniakea-elixir-it.github.io/laniakea_at_recas){: .btn .btn-primary .trim-p}
diff --git a/content/elixir-it/main5.md b/content/elixir-it/main5.md new file mode 100644 index 0000000000..69a9da30ca --- /dev/null +++ b/content/elixir-it/main5.md @@ -0,0 +1,62 @@ +--- +title: Galaxy Italy +subtitle: Laniakea on-demand platform +--- + +# Communities: Laniakea's public servers + +
+
+
+

Vinyl

+

VINYL (Variant prIoritizatioN bY survivaL analysis) integrates an innovative method for variant prioritization, along with a highly curated collection of databases and resources for the annotation of human genetic variants.

+
+
+ Vinyl +


+ Vinyl +
+
+
+
+
+

CorGAT

+

CorGAT, the Coronavirus Genome Analysis Tool, is a novel, highly effective and user-friendly approach for the functional annotation of SARS-CoV-2 genomes based on Galaxy.

+
+

+ CorGAT +


+ CorGAT +
+
+
+
+
+

ITSoneWB

+

ITSoneWB (ITSone WorkBench) collects and integrates the high-quality ITS1 reference collection in ITSoneDB with DNA metabarcoding well-established analysis pipelines and new tools in an easy-to-use service addressing the eukaryotic domain of life.

+
+ ITSoneWB +


+ ITSoneWB +
+
+
+
+
+
+
+

PIPE-T

+

PIPE-T is the first Galaxy tool for parsing, filtering, normalising, imputing, and analysing RT-qPCR data. PIPE-T integrates the functionalities implemented in various R packages, such as HTqPCR, impute, and RankProd, in a simple, transparent, accessible, reproducible, and user-friendly environment.

+
+
+ Vinyl +

+ Pipe-T +
+
+
+
+
+
+
+
diff --git a/content/elixir-it/navbar.yml b/content/elixir-it/navbar.yml index b1a4c92a13..e5621de53c 100644 --- a/content/elixir-it/navbar.yml +++ b/content/elixir-it/navbar.yml @@ -1,5 +1,6 @@ style: color: "#2c81bb" + #lightBg: true left: - label: News relativeTo: subsite @@ -8,7 +9,11 @@ left: relativeTo: subsite target: events/ - label: People - target: https://usegalaxy-eu.github.io/elixir-it/people + relativeTo: subsite + target: people/ + - label: Cite + relativeTo: subsite + target: cite/ right: - label: Help contents: diff --git a/content/elixir-it/news/main.md b/content/elixir-it/news/main.md index 2e9659adfd..6034938e37 100644 --- a/content/elixir-it/news/main.md +++ b/content/elixir-it/news/main.md @@ -1,5 +1,5 @@ --- -title: ELIXIR-IT/Laniakea Galaxy News +title: Galaxy Italy News --- news diff --git a/content/elixir-it/people/index.md b/content/elixir-it/people/index.md new file mode 100644 index 0000000000..c036ddf8bd --- /dev/null +++ b/content/elixir-it/people/index.md @@ -0,0 +1,50 @@ +--- +title: Galaxy Italy Team +--- + +
+ +
+ +
+

Federico Zambelli

+

ELIXIR-Italy technical coordinator and Galaxy Italy team leader

+ + + +
+
+ +
+ +
+

Marco Antonio Tangaro

+

UseGalaxy.it and Laniakea lead developer

+ + + +
+
+ +
+ +
+

Luigi Mansi

+

UseGalaxy.it and Laniakea developer

+ +
+
+ +
+ +
+

Gaetanomaria De Sanctis

+

UseGalaxy.it and Laniakea developer

+ +
+
+ + + +
diff --git a/content/elixir-it/site-footer.md b/content/elixir-it/site-footer.md index 6c1d93cf38..134182c94b 100644 --- a/content/elixir-it/site-footer.md +++ b/content/elixir-it/site-footer.md @@ -1,13 +1,32 @@ +

+ +
+ +[![](https://raw.githubusercontent.com/Laniakea-elixir-it/resources/master/logos/elixir_italy_white_background.png)](https://elixir-italy.org/) +[![](https://raw.githubusercontent.com/Laniakea-elixir-it/resources/refs/heads/master/logos/logo_CNR_compatto.png)](https://www.cnr.it/en) +[![](https://github.com/Laniakea-elixir-it/resources/blob/master/logos/INFN.png?raw=true)](https://www.ba.infn.it/it/) +[![](https://github.com/Laniakea-elixir-it/resources/blob/master/logos/ReCaS-Bari.png?raw=true)](https://www.recas-bari.it/index.php/en/) +[![](https://work.unimi.it/aree_protette/cataloghi/ATENEO/MARCHI/jpg/ATENEO-09.jpg)](https://www.unimi.it/en) +[![](https://www.uniba.it/it/dati-homepage/logo_UNIBA.png)](https://www.uniba.it/en) +[![](https://www.garr.it/it/news-e-eventi/pubblicazioni/materiale-informativo/loghi/3955-logo-garr-png/file)](https://www.garr.it/en/) +[![](https://www.cineca.it/sites/default/files/2024-07/logo-cineca.png)](https://www.cineca.it/en) + +
+ +
+
-[Laniakea](https://laniakea-elixir-it.github.io) has been developed in the framework of the [INDIGO-Datacloud](https://www.indigo-datacloud.eu) project funded by the European Commision H2020 research and innovation program under grant agreement RIA 653549. +[UseGalaxy.it](https://usegalaxy.it) has been developed in the framework of the [EuroScienceGateway](https://galaxyproject.org/projects/esg/) funded by the European Union programme Horizon Europe (HORIZON-INFRA-2021-EOSC-01-04) under grant agreement number 101057388 and by UK Research and Innovation (UKRI) under the UK government’s Horizon Europe funding guarantee grant number 10038963. + +The [UseGalaxy.it](https://usegalaxy.it) service is provided with the support of [ELIXIR-ITALY](https://elixir-italy.org), [ReCaS-Bari](https://www.recas-bari.it), [](), [Consortium GARR](https://www.garr.it/en/), [CINECA](https://www.cineca.it/en) and [University of Milan](https://www.unimi.it/en). -The development of Laniakea continues in the framework of [EOSC-Pillar](https://www.eosc-pillar.eu) (Grant agreement ID: 857650) and [EOSC-Life](https://www.eosc-life.eu) (Grant agreement ID: 824087) H2020 projects. +[Laniakea](https://laniakea-elixir-it.github.io) has been developed in the framework of the [INDIGO-Datacloud](https://www.indigo-datacloud.eu) project funded by the European Commision H2020 research and innovation program under grant agreement RIA 653549. The development of Laniakea continued in the framework of [EOSC-Pillar](https://www.eosc-pillar.eu) (Grant agreement ID: 857650) and [EOSC-Life](https://www.eosc-life.eu) (Grant agreement ID: 824087) H2020 projects. The [Laniakea@ReCaS](https://laniakea-elixir-it.github.io/laniakea_at_recas) service is provided with the support of [ELIXIR-ITALY](https://elixir-italy.org) and [ReCaS-Bari](https://www.recas-bari.it). [](){: .fab .fa-github style="color: #777"} [Edit this page on GitHub](https://github.com/galaxyproject/galaxy-hub/blob/master/content/bare/elixir-it/galaxy/index.md)   -[](){: .fa .fa-envelope style="color: #777"} [laniakea.helpdesk@gmail.com](mailto:laniakea.helpdesk@gmail.com)   +[](){: .fab .fa-github style="color: #777"} [UseGalaxy-it](https://github.com/usegalaxy-it/)   [](){: .fab .fa-github style="color: #777"} [Laniakea-elixir-it](https://github.com/Laniakea-elixir-it)   [](){: .fa .fa-rss style="color: #777"} Subscribe [via RSS (UseGalaxy.eu Feed)](/eu/feed.atom) diff --git a/content/events/2025-02-04-spoc_meet/index.md b/content/events/2025-02-04-spoc_meet/index.md new file mode 100644 index 0000000000..e5d6dc6a2d --- /dev/null +++ b/content/events/2025-02-04-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-02-04' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-02-13-gcb_meet/index.md b/content/events/2025-02-13-gcb_meet/index.md new file mode 100644 index 0000000000..9cfea4b885 --- /dev/null +++ b/content/events/2025-02-13-gcb_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Galaxy Community Board Meeting: 🪑GCB" +date: '2025-02-13' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +[SIG representatives](https://galaxyproject.org/community/sig/) are welcome to join the quarterly meeting of the Galaxy Community Board! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +In each Galaxy Community Board meeting, we focus on a particular task or need from the SIG chairs. We work collectively to drive Galaxy development to serve our communities - so make sure your community is represented! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-03-06-spoc_meet/index.md b/content/events/2025-03-06-spoc_meet/index.md new file mode 100644 index 0000000000..341c87c579 --- /dev/null +++ b/content/events/2025-03-06-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-03-06' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-04-01-gcb_meet/index.md b/content/events/2025-04-01-gcb_meet/index.md new file mode 100644 index 0000000000..b836267b2c --- /dev/null +++ b/content/events/2025-04-01-gcb_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Galaxy Community Board Meeting: 🪑GCB" +date: '2025-04-01' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +[SIG representatives](https://galaxyproject.org/community/sig/) are welcome to join the quarterly meeting of the Galaxy Community Board! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +In each Galaxy Community Board meeting, we focus on a particular task or need from the SIG chairs. We work collectively to drive Galaxy development to serve our communities - so make sure your community is represented! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-04-08-spoc_meet/index.md b/content/events/2025-04-08-spoc_meet/index.md new file mode 100644 index 0000000000..95c377ce0b --- /dev/null +++ b/content/events/2025-04-08-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-04-08' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-05-06-spoc_meet/index.md b/content/events/2025-05-06-spoc_meet/index.md new file mode 100644 index 0000000000..58b4f6ee02 --- /dev/null +++ b/content/events/2025-05-06-spoc_meet/index.md @@ -0,0 +1,27 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-05-06' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- + +The [Small Scale Galaxy Admins group](https://galaxyproject.org/community/sig/small-scale-admins/) is a [Galaxy community of practice](https://galaxyproject.org/community/sig/#communities-of-practice). +The meetings are taking place every month and are listed in the [Galaxy WG calendar](https://calendar.google.com/calendar/u/0/embed?src=5l6o0msfduoir59hrab0jlkocc@group.calendar.google.com). diff --git a/content/events/2025-06-03-gcb_meet/index.md b/content/events/2025-06-03-gcb_meet/index.md new file mode 100644 index 0000000000..d3b5e7ce93 --- /dev/null +++ b/content/events/2025-06-03-gcb_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Galaxy Community Board Meeting: 🪑GCB" +date: '2025-06-03' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +[SIG representatives](https://galaxyproject.org/community/sig/) are welcome to join the quarterly meeting of the Galaxy Community Board! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +In each Galaxy Community Board meeting, we focus on a particular task or need from the SIG chairs. We work collectively to drive Galaxy development to serve our communities - so make sure your community is represented! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-06-05-spoc_meet/index.md b/content/events/2025-06-05-spoc_meet/index.md new file mode 100644 index 0000000000..2fa718fcfa --- /dev/null +++ b/content/events/2025-06-05-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-06-05' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-07-01-spoc_meet/index.md b/content/events/2025-07-01-spoc_meet/index.md new file mode 100644 index 0000000000..48f7c5b284 --- /dev/null +++ b/content/events/2025-07-01-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-07-01' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-08-05-spoc_meet/index.md b/content/events/2025-08-05-spoc_meet/index.md new file mode 100644 index 0000000000..3f20e8fb39 --- /dev/null +++ b/content/events/2025-08-05-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-08-05' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-09-04-spoc_meet/index.md b/content/events/2025-09-04-spoc_meet/index.md new file mode 100644 index 0000000000..1ff4481244 --- /dev/null +++ b/content/events/2025-09-04-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-09-04' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-09-09-gcb_meet/index.md b/content/events/2025-09-09-gcb_meet/index.md new file mode 100644 index 0000000000..741101f320 --- /dev/null +++ b/content/events/2025-09-09-gcb_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Galaxy Community Board Meeting: 🪑GCB" +date: '2025-09-09' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +[SIG representatives](https://galaxyproject.org/community/sig/) are welcome to join the quarterly meeting of the Galaxy Community Board! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +In each Galaxy Community Board meeting, we focus on a particular task or need from the SIG chairs. We work collectively to drive Galaxy development to serve our communities - so make sure your community is represented! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-10-07-spoc_meet/index.md b/content/events/2025-10-07-spoc_meet/index.md new file mode 100644 index 0000000000..b57b2faa79 --- /dev/null +++ b/content/events/2025-10-07-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-10-07' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-11-04-spoc_meet/index.md b/content/events/2025-11-04-spoc_meet/index.md new file mode 100644 index 0000000000..f3f099fd23 --- /dev/null +++ b/content/events/2025-11-04-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-11-04' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-11-13-gcb_meet/index.md b/content/events/2025-11-13-gcb_meet/index.md new file mode 100644 index 0000000000..f622f339da --- /dev/null +++ b/content/events/2025-11-13-gcb_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Galaxy Community Board Meeting: 🪑GCB" +date: '2025-11-13' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: communities +subsites: [all-eu, global, us] +--- + +[SIG representatives](https://galaxyproject.org/community/sig/) are welcome to join the quarterly meeting of the Galaxy Community Board! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +In each Galaxy Community Board meeting, we focus on a particular task or need from the SIG chairs. We work collectively to drive Galaxy development to serve our communities - so make sure your community is represented! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/events/2025-12-04-spoc_meet/index.md b/content/events/2025-12-04-spoc_meet/index.md new file mode 100644 index 0000000000..c52f6bd301 --- /dev/null +++ b/content/events/2025-12-04-spoc_meet/index.md @@ -0,0 +1,24 @@ +--- +title: "Single-cell & sPatial Omics Community Meeting: 🖖🏾SPOC" +date: '2025-12-04' +days: 1 +continent: GL +location: + name: Online, Global +gtn: false +contact: Wendi Bacon +tags: single-cell +subsites: [all-eu, global, us] +--- + +Join the us for our monthly meeting! Our meeting times roll across months to ensure at least one meeting is work-day friendly for anyone on the planet. + +We discuss what people are working on (often preventing work duplication globally!), welcome new members, and brainstorm all things 🖖🏾Single-cell & sPatial Omics in Galaxy! + +You can check out our 📝rolling meeting notes to see our upcoming agenda, or read about us in our Galaxy Community Hub page. + +👋🏾Hope to see you there! + + + +--- diff --git a/content/images/logos/usegalaxy-it.png b/content/images/logos/usegalaxy-it.png new file mode 100644 index 0000000000..9188a9100b Binary files /dev/null and b/content/images/logos/usegalaxy-it.png differ diff --git a/content/news/2024-12-12-DecemberNewsletter/GBCC2025.png b/content/news/2024-12-12-DecemberNewsletter/GBCC2025.png new file mode 100644 index 0000000000..06a8b69a37 Binary files /dev/null and b/content/news/2024-12-12-DecemberNewsletter/GBCC2025.png differ diff --git a/content/news/2024-12-12-DecemberNewsletter/GTA.jpg b/content/news/2024-12-12-DecemberNewsletter/GTA.jpg new file mode 100644 index 0000000000..55513c732e Binary files /dev/null and b/content/news/2024-12-12-DecemberNewsletter/GTA.jpg differ diff --git a/content/news/2024-12-12-DecemberNewsletter/GalaxyNews.png b/content/news/2024-12-12-DecemberNewsletter/GalaxyNews.png new file mode 100644 index 0000000000..c95108c538 Binary files /dev/null and b/content/news/2024-12-12-DecemberNewsletter/GalaxyNews.png differ diff --git a/content/news/2024-12-12-DecemberNewsletter/GroupPhoto3.JPG b/content/news/2024-12-12-DecemberNewsletter/GroupPhoto3.JPG new file mode 100644 index 0000000000..cd3d7c70f7 Binary files /dev/null and b/content/news/2024-12-12-DecemberNewsletter/GroupPhoto3.JPG differ diff --git a/content/news/2024-12-12-DecemberNewsletter/gcc2024-banner.png b/content/news/2024-12-12-DecemberNewsletter/gcc2024-banner.png new file mode 100644 index 0000000000..f977e0eb9f Binary files /dev/null and b/content/news/2024-12-12-DecemberNewsletter/gcc2024-banner.png differ diff --git a/content/news/2024-12-12-DecemberNewsletter/index.md b/content/news/2024-12-12-DecemberNewsletter/index.md new file mode 100644 index 0000000000..2fa2b78a18 --- /dev/null +++ b/content/news/2024-12-12-DecemberNewsletter/index.md @@ -0,0 +1,233 @@ +--- +title: "Galaxy Newsletter: December 2024" +tease: "From groundbreaking milestones to exciting new features, join us in celebrating Galaxy’s incredible journey through 2024! Plus, get a sneak peek at what Galaxy has in store for 2025." +hide-tease: false +authors: "Natalie Whitaker-Allen" +date: "2024-12-12" +tags: ["highlight"] +subsites: [global,all] +--- + +![Galaxy News](GalaxyNews.png) + +December 2024 + +Hello, Galaxy Community + +As we close out 2024, we are grateful for each of you who engaged with us this year, whether through training sessions, conferences, research initiatives, or as part of the Galaxy community at large. This year's final newsletter celebrates the major achievements, events, and milestones that have strengthened our community. It’s been a remarkable year of growth, learning, and impact across various scientific domains. + +Thank you for tuning in and for being a part of Galaxy! + +--- + +# **Galaxy 2024 Milestones** + +2024 has been a landmark year for Galaxy\! This year, we celebrated a significant milestone with over [**20,000 research citations**](https://scholar.google.com/citations?hl=en&user=3tSiRGoAAAAJ) referencing Galaxy, a testament to the platform’s pivotal role in advancing research across multiple scientific disciplines. Additionally, we celebrated the achievement of reaching over **500k registered users** across all UseGalaxy servers\! + +Other major milestones from the year include: + +* Over **20,000 interactions on GitHub**, highlighting the active development and collaboration within the Galaxy ecosystem. +* Galaxy EU reached over **100,000 users**. +* On YouTube, Galaxy content reached new heights with **620,000 impressions**, **58,000 views**, and over **4,500 hours of content watched** in 2024 alone. +* Galaxy AU hit over **10 million jobs**. +* The [Galaxy Training Network](https://training.galaxyproject.org/training-material/) celebrated the release of their **400th tutorial**. + +These milestones reflect the dedication of our global community and the growing influence of Galaxy in fostering open science, education, and innovation. + +--- + +# **Galaxy Releases in 2024: Key Updates and Features** + +2024 has been an exciting year for Galaxy, with a host of new features and enhancements that make data analysis, collaboration, and sharing more intuitive and efficient. Here are some highlights from this year’s releases: + +* **ColabFold on Galaxy**: Galaxy now supports ColabFold, enabling ultra-fast **protein structure prediction** by combining MMseqs2 with AlphaFold2 or RoseTTAFold. This powerful tool splits the process into two streamlined steps: Multiple Sequence Alignment (MSA) and AlphaFold2 predictions, offering speed, accuracy, and iterative refinement options—all within the Galaxy environment. + +* **Workflow Comments**: Collaboration within workflows is now easier than ever with the new Workflow Comments feature in the Galaxy Workflow Editor. Add **text comments, markdown explanations, and even freehand drawings** to enhance communication and improve workflow structure and organization. + +* **Enhanced Published Workflow Sharing**: Sharing workflows has been revolutionized with a redesigned Published Workflow Sharing page. The updated layout includes a read-only mode, an embedded interactive editor view, and improved responsiveness, making it more straightforward for users to **share, navigate, and collaborate on workflows**. + +* **Seamless InvenioRDM Integration**: Galaxy now integrates directly with InvenioRDM, allowing users to **import files** from InvenioRDM repositories into Galaxy and **publish Galaxy records** (like Histories and datasets) to InvenioRDM. This integration streamlines data import/export processes, offering greater flexibility and efficiency. + +* **Activity Bar Enabled by Default**: The Activity Bar is now enabled by default, providing users with **quick access to essential features** and improving overall workflow navigation. + +* **Workflow Invocation Graph View**: The new **graph view** in the workflow invocation summary clearly represents job states for each workflow step. Clicking on a step reveals detailed information, **improving monitoring and troubleshooting** capabilities. + +* **Zenodo Integration**: The Zenodo file source plugin simplifies integration with Zenodo and Invenio repositories. New schemes (`invenio://` and `zenodo://`) enhance alignment with these platforms while maintaining support for existing exports using `gxfiles://`. + +These updates are a testament to Galaxy’s commitment to improving user experience, enhancing collaboration, and supporting seamless data sharing. We’re excited to see how the community uses these new features to advance their research and workflows\! + +--- + +![GCC2024](gcc2024-banner.png) + +# **Galaxy Community Conference 2024** + +The [**Galaxy Community Conference 2024**](https://galaxyproject.org/news/2024-07-19-gc-c2024-meeting-report/) **(GCC2024)** brought together **151 participants from 28 countries** in Brno, Czech Republic, for a dynamic and collaborative event celebrating the Galaxy ecosystem. This year’s conference featured **54 talks**, **55 posters and demos**, **14 Birds of a Feather sessions**, and two days of **Collaboration Fest (CoFest)**, where attendees advanced projects and strengthened the Galaxy platform. + +The conference showcased Galaxy’s global impact with **three inspiring keynote speakers**: + +* **Jana Klánová** shared insights on exposomics and environmental health. +* **Ute Gunsenheimer** discussed the European Open Science Cloud (EOSC) and FAIR principles. +* **Daria Onichtchouk** highlighted Galaxy’s role in zebrafish research and developmental biology. + +The program offered dual tracks—**Analysis** and **Enablement**—featuring cutting-edge research, tool development, and community outreach efforts. **Tailored training sessions** provided hands-on learning for new users, educators, tool developers, and system administrators. + +**Networking and community building** were at the heart of GCC2024, with social events like walking tours, a VENUS (Women & Nonbinary Empowerment) lunch, and a memorable conference dinner at the historic Augustinian Abbey. + +The conference also spotlighted six exceptional fellowship recipients, supported by the **JXTX \+ GCC2024 Scholarship**, who shared their innovative research through talks and posters. + +In the collaborative spirit of Galaxy, CoFest participants initiated projects such as a **workflow-centric landing page** and subdomain unification for regional servers, ensuring continued innovation. + +![Group Photo](GroupPhoto3.JPG) + +As we celebrate the success of GCC2024, we thank the participants, organizers, and sponsors who made this event possible. Stay tuned for next year's milestone Galaxy event\! + +--- + +# **Galaxy Training Academy 2024** + +The Galaxy Training Academy 2024 was a global success. From October 7th to 11th, over 2,800 registered participants participated in an asynchronous, self-paced learning event. + +![GTA 2024](GTA.jpg) + +This year’s Academy featured **eight scientific tracks**, each offering individualized learning paths: + +* **Proteomics** +* **Assembly** +* **Transcriptomics** +* **Single-cell analysis** +* **Microbiome research** +* **Bacterial genomics** +* **BY-COVID** +* **Machine learning** + +Participants could dive deep into these domains with curated tutorials and pre-recorded lectures while benefiting from **24/7 support on Slack**. The Academy started with an introductory day designed to help new users get familiar with Galaxy or enhance foundational skills through interactive activities like the **Data Manipulation Olympics**. The week concluded with a **"choose your own adventure"** format, offering access to the entire GTN training library and a FAIR (Findable, Accessible, Interoperable, and Reusable) training to promote open science. + +This event was made possible by the dedication of the **GTN community**, with **80 contributors** updating **53 tutorials**, producing **27 new training videos**, and hosting **24 expert speakers**. Popular tracks included **Transcriptomics**, **Assembly**, and **Machine Learning**, and participants gave high marks to the engaging content and real-time support. + +**Plans for the Future** + +Missed the event? No problem\! The training materials remain available online and will continue to be updated. Looking ahead, we’re already planning the next Galaxy Training Academy for **Spring 2025**, where we aim to expand on this year’s success with new tracks, updated materials, and even more opportunities for global collaboration. + +Thank you to everyone who participated in and contributed to the Galaxy Training Academy 2024\. Your enthusiasm and support make events like this possible, and we can’t wait to see you next year\! + +--- + +# **Other 2024 Events** + +Galaxy was featured at numerous conferences throughout the year, reflecting our **interdisciplinary reach and adaptability**. Here’s a closer look at some of the key events where Galaxy shined: + +* Biological Data Science 2024 +* Anvil Community Conference +* Sc-verse Conference +* Gateways 2024 +* Biology of Genomes +* Advances in Genome Biology and Technology +* PAG2024 + +Galaxy’s robust training lineup this year covered critical topics, from **introductory sessions to advanced techniques**, ensuring that researchers and professionals alike could strengthen their Galaxy skills. Below are some of our 2024 workshops, each of which provided participants with practical, hands-on experience: + +* An Introduction to **HighPerformance Computing** +* Exploring the Galaxy Application for Data Sciences +* Workshop in **High-Throughput Data Analysis** +* Awareness in **Data Management and Analysis** for Industry and Research +* de.NBI Galaxy Training Course - **RNAseq Analysis** +* Making Clinical Dataset **FAIR** +* An Introduction to Scaffolding with **Hi-C Data** in Galaxy +* FAIR data management in **single-cell analysis** +* Strategies for training and knowledge exchange with a consulting perspective +* Get Started with Galaxy +* A practical introduction to **bioinformatics and RNA-seq** using Galaxy +* Webinar on data management with **DataHub** +* **BRC Analytics** Webinar +* Galaxy for **Oceanographic** Insights + +These sessions collectively equipped participants with critical skills, from data management and analysis to the application of Galaxy in specialized fields. We look forward to continuing more training offerings in 2025 and beyond\! + +--- + +# **Upcoming: Galaxy and Bioconductor Community Conference 2025 (GBCC2025)** + +We’re already gearing up for the first-ever **Galaxy and Bioconductor Community Conference 2025 (GBCC2025)**, where we’ll bring together experts, practitioners, and enthusiasts from the Galaxy and Bioconductor communities. This conference represents a unique convergence of two powerful open-source bioinformatics platforms, allowing attendees to dive deep into shared advancements, collaborative projects, and community-led developments. + +![GBCC2025](GBCC2025.png) + +**Why GBCC2025?** +GBCC2025 represents the convergence of two powerful open-source bioinformatics platforms, Galaxy and Bioconductor. By combining their strengths, this conference will foster a deeper understanding of their shared advancements, facilitate collaborative projects, and highlight community-led developments that drive impactful research. + +**What to Expect:** + +* **Keynote Talks:** Inspiring speakers from the Galaxy and Bioconductor communities will share insights into cutting-edge research and advancements. +* **Collaborative Workshops:** Hands-on sessions to enhance skills, build workflows, and solve real-world bioinformatics challenges. +* **Networking Opportunities:** Connect with researchers, developers, and educators who share your passion for open science. + +**Get Involved\!** +The GBCC2025 Logo Design Contest has officially concluded, and we’re excited to reveal the winning logo soon—stay tuned\! + +We’re also **seeking volunteers to join the Scientific Committee**, where members will play a vital role in reviewing abstract submissions and shaping the scientific program. If you’re passionate about supporting open science and want to contribute to GBCC2025 in a meaningful way, we’d love to hear from you\! [Please register your interest using this form.](https://docs.google.com/forms/d/e/1FAIpQLSefPmRCOb5cothVs1VJeTuP7mCvLijoQNuVs26KPdy2KGHfxA/viewform) + +Whether you’re a Galaxy user, a Bioconductor enthusiast, or new to both platforms, GBCC2025 promises to be an inclusive and engaging conference that **bridges communities and inspires innovation**. Save the date, and stay tuned for updates as we continue to unveil more details about this exciting event. + +--- + +# **Galaxy in Research** + +Looking back on 2024, we’re excited to celebrate the new recurring feature in our News section: *Galaxy in Research*. This series has **spotlighted new and exciting studies from around the world**, showcasing how researchers leverage Galaxy to tackle complex scientific questions. From population genetics to structural biology, these stories have not only highlighted the versatility of Galaxy but also the incredible innovations of our community. We hope you’ve enjoyed these features as much as we’ve loved sharing them\! + +[**Galaxy in Research: Transforming life in the tropics using genomic technologies for One Health**](https://galaxyproject.org/news/2024-11-21-galaxy-in-research-calcino2024/) +*How can genomics improve health, food production, and biodiversity in tropical regions? A new review explores how cutting-edge technologies, including Galaxy, are shaping a sustainable future for the tropics.* + +[**Galaxy in Research: Microbial life at Arctic hydrothermal vents**](https://galaxyproject.org/news/2024-10-30-galaxy-in-research/) +*How do hydrothermal vents at the bottom of the Arctic Ocean fuel microbial life? A new study explores the microbial ecosystems thriving at the Aurora and Polaris seamounts, revealing key insights into how hydrogen and sulfur power deep-sea life.* + +[**Galaxy in Research: New insights into antibody activation using AlphaFold in Galaxy**](https://galaxyproject.org/news/2024-10-01-galaxy-in-reseach-degn/) +*How do antigens trigger B-cell receptors (BCRs), and can a single mechanism explain the activation of all BCR types? This study explores a unifying model that integrates various mechanisms of BCR triggering, providing fresh perspectives on antibody activation.* + +[**Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics**](https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/) +*A new study has sequenced and analyzed two wild loquat chloroplast genomes, revealing key insights into their evolutionary history and the genetic diversity of loquat species.* + +[**Galaxy in Research: Advancing quantum materials research with Galaxy**](https://galaxyproject.org/news/2024-19-08-galaxy-in-research/) +*At Oak Ridge National Laboratory, scientists have harnessed the power of Galaxy to bring together cutting-edge computing resources, paving the way for new discoveries in quantum materials through advanced neutron scattering data analysis.* + +[**Galaxy in Research: Exploring DNA methylation and aging across diverse human tissues**](https://galaxyproject.org/news/2024-08-14-galaxy-in-research/) +*How does DNA methylation correlate with aging across different human tissues? A new study provides insights into this question, revealing tissue-specific and shared epigenetic patterns.* + +[**Galaxy in Research: Exploring Genetic Variability in Almond Blooming**](https://galaxyproject.org/news/2024-07-30-galaxy-in-research-mir/) +*Learn how genetic variations influence the blooming periods of almond cultivars, revealing key insights into their molecular regulation.* + +[**Galaxy in Research: Unlocking genetic secrets of Lake Baikal’s endemic sponges**](https://galaxyproject.org/news/2024-07-17-galaxy-in-research/) +*Explore the depths of Lake Baikal and discover how cutting-edge genetic research in Galaxy is unraveling the complex relationships between its unique sponge species.* + +[**Galaxy in Research: Molecular secrets of minnow adaptation to salinity stress**](https://galaxyproject.org/news/2024-07-03-galaxy-in-research/) +*Discover how advanced transcriptomic analyses in Galaxy reveal the intricate molecular adaptations of minnows to freshwater salinization.* + +[**Galaxy in Research: Decoding chromatin interactions with asteRIa**](https://galaxyproject.org/news/2024-06-05-galaxy-in-research/) +*Find out how Galaxy helps researchers unlock the mysteries of gene expression regulation through chromatin studies.* + +[**Galaxy in Research: Investigating Food Safety Threats**](https://galaxyproject.org/news/2024-06-03-galaxy-in-research/) +*Learn how Galaxy can be used to detect and analyze drug-resistant bacteria threatening food safety in Egypt.* + +[**Galaxy in Research: Exploring the Hidden World of Antarctic Toxins with Galaxy**](https://galaxyproject.org/news/2024-05-14-galaxy-in-research/) +*Discover how Galaxy is helping to unravel the hidden world of peptide toxins in an Antarctic marine invertebrate.* + +--- + +# **Upcoming Events** + +| DATE | EVENT | VENUE/LOCATION | +| :---- | :---- | :---- | +| 19 December 2024 | [Small Scale Galaxy Admins Meeting](https://galaxyproject.org/events/2024-12-small-scale/) | Online, Global | +| 10–15 January 2025 | [Plant and Animal Genome Conference (PAG32)](https://www.intlpag.org/2025/) | San Diego, CA, USA | +| 16 January 2025 | [Small Scale Galaxy Admins Meeting](https://galaxyproject.org/events/2025-01-small-scale/) | Online, Global | +| 20 February 2025 | [Small Scale Galaxy Admins Meeting](https://galaxyproject.org/events/2025-02-small-scale/) | Online, Global | +| 10–14 March 2025 | [Workshop on high-throughput sequencing data analysis with Galaxy](https://galaxyproject.org/events/2025-03-10-galaxy-workshop-freiburg/) | University of Freiburg, Germany | +| 12–14 March 2025 | [E-Science-Tage 2025](https://galaxyproject.org/events/2025-03-12-e-science/) | Heidelberg, Germany | +| 27 April – 1 May 2025 | [European Geosciences Union (EGU) 2025](https://galaxyproject.org/events/2024-10-24-egu2025/) | Vienna, Austria | +| 23–26 June 2025 | [Galaxy and Bioconductor Community Conference (GBCC2025)](https://galaxyproject.org/news/2024-09-03-gbc-c2025/) | Cold Spring Harbor, NY, USA | + +--- + +*Thank you for being a part of Galaxy\!* + +**Get more timely info by following us on [Mastodon](https://mastodon.social/@galaxyproject@mstdn.science), [Bluesky](https://bsky.app/profile/galaxyproject.bsky.social), and [LinkedIn](https://www.linkedin.com/company/galaxy-project)\!** + diff --git a/content/news/2024-12-18-SPOC_Year_in_Review/index.md b/content/news/2024-12-18-SPOC_Year_in_Review/index.md new file mode 100644 index 0000000000..cfdc6514ff --- /dev/null +++ b/content/news/2024-12-18-SPOC_Year_in_Review/index.md @@ -0,0 +1,21 @@ +--- +authors: "Wendi Bacon" +date: '2024-12-18' +external_url: https://training.galaxyproject.org/training-material/news/2024/12/18/spoc.html +main_subsite: global +subsites: +- all +tags: +- training +- gtn-news +- news +- gtn +- single-cell +tease: "As we orbit the end of another stellar year, let’s engage warp drive and reflect on the out-of-this-world achievements of the **Single-cell & sPatial Omics Community (SPOC 🖖)**. From launching new tools to charting new tutorials, SPOC’s journey through the Galaxy (platform) has been nothing short of cosmic! 🌠" +title: "🚀 2024: A SPOC-tacular Year in Review 🌌" + +--- +🌌 Looking to the Horizon +As SPOC’s starship accelerates toward 2025, we’ll continue to explore new omics territories and deepen our cosmic connections across the Galaxy. Thank you to every SPOC cadet, captain, and commander who contributed this year—you’ve made SPOC the brightest star in the bioinformatics universe! + +Keep reaching for the stars, SPOC-nauts! 🪐✨ diff --git a/content/news/2025-01-07-microgalaxy-preprint/graphical_abstract.png b/content/news/2025-01-07-microgalaxy-preprint/graphical_abstract.png new file mode 100644 index 0000000000..3a67a55613 Binary files /dev/null and b/content/news/2025-01-07-microgalaxy-preprint/graphical_abstract.png differ diff --git a/content/news/2025-01-07-microgalaxy-preprint/index.md b/content/news/2025-01-07-microgalaxy-preprint/index.md new file mode 100644 index 0000000000..812d2cf7da --- /dev/null +++ b/content/news/2025-01-07-microgalaxy-preprint/index.md @@ -0,0 +1,51 @@ +--- +title: "Unlocking Microbial Data Analysis: The microGalaxy Preprint Is Here!" +date: '2024-01-07' +tags: [paper] +subsites: [eu, fr, freiburg, global, all] +--- + +We are thrilled to announce the release of our preprint, **"microGalaxy: A gateway to tools, workflows, and training for accessible, reproducible, and FAIR microbial data analysis,"** now available on [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1.full.pdf)! + +Overview of microGalaxy's applications across Environment, Health, and Agri-Food domains, supporting DNA, RNA, protein, and metabolite analysis. Key topics include biogeochemical cycles, antimicrobial resistance, and pathogen monitoring. Centered on One Health, the platform integrates 220+ tool suites, 65+ workflows, and 45+ tutorials, promoting FAIR principles, citizen science, and education. + +This work represents a significant step forward in making microbial research accessible to a broader community. The microGalaxy platform integrates cutting-edge tools, workflows, and training resources designed specifically for microbial data analysis. It's built on the FAIR (Findable, Accessible, Interoperable, and Reusable) principles, ensuring that researchers can not only perform robust analyses but also share and reuse their data with confidence. + +### What is microGalaxy? + +microGalaxy is an ecosystem of Galaxy tools, workflows and training dedicated to microbial research. The platform provides: + +- **Community-curated tools** for outine and real-world microbial research practice +- **Ready-to-use workflows** for various microbial research applications. +- **Training materials** to empower researchers, regardless of their computational background. +- **A community-driven approach** to ensure continuous development and innovation. + +It is hosted on Galaxy Europe Serveur ([microgalaxy.usegalaxy.eu](https://microgalaxy.usegalaxy.eu/)) for now and soon on other UseGalaxy.* + +The preprint highlights how microGalaxy bridges the gap between advanced bioinformatics methods and researchers tackling complex microbial questions. + +### Key Highlights + +- **Comprehensive Workflows**: From genome assembly to metagenomic analysis, microGalaxy offers workflows tailored for diverse microbial datasets. +- **FAIR Principles in Action**: The platform ensures that all tools and workflows adhere to FAIR guidelines, promoting transparency and collaboration. +- **Training and Support**: Extensive training materials and community support make it easy for researchers to get started and expand their expertise. +- **Comparison of Platforms**: The preprint includes a detailed table comparing microGalaxy's features to those of other microbial data analysis platforms, showcasing its unique capabilities. + +### Why It Matters + +Microbial research is at the forefront of addressing critical challenges in health, agriculture, and environmental sustainability. By providing a robust and reproducible platform, microGalaxy empowers researchers to: + +- Explore microbial ecosystems more effectively. +- Share and reuse data and workflows seamlessly. +- Foster collaboration across disciplines and institutions. + +### Get Involved + +We'd love to hear your feedback! Explore the preprint below (and on [bioRXiV](https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1.full.pdf)), try out the microGalaxy platform ([microgalaxy.usegalaxy.eu](https://microgalaxy.usegalaxy.eu/)), and join our growing [community](/community/sig/microbial) of microbial researchers. + +Stay tuned for more updates as we work towards publishing this exciting research and further developing the microGalaxy ecosystem. Together, we can advance microbial research and tackle global challenges with cutting-edge science and technology. + +Let us know what you think by tagging us on Bluesky ([@galaxyproject.bsky.social](https://bsky.app/profile/galaxyproject.bsky.social)), Mastodon ([@galaxyproject@mstdn.science](https://mstdn.science/@galaxyproject)), [LinkedIn](https://www.linkedin.com/company/galaxy-project/) or by joining the conversation on [our microGalaxy Matrix channel](https://matrix.to/#/#galaxyproject_microGalaxy:gitter.im). + + + diff --git a/cypress/integration/accessibility.spec.js b/cypress/integration/accessibility.spec.js index ca0d81c6d8..eb8774c38c 100644 --- a/cypress/integration/accessibility.spec.js +++ b/cypress/integration/accessibility.spec.js @@ -30,11 +30,4 @@ describe("Accessibility Testing", () => { cy.wait(500); cy.checkA11y("#app", CYPRESS_ACCESSIBILITY_CONFIG); }); - it(`GCC${CURRENT_DATE.getUTCFullYear()} page has no detectable a11y violations on load`, () => { - cy.visit(`/events/gcc${CURRENT_DATE.getUTCFullYear()}/`).get("#app").injectAxe(); - // Ensure masthead has loaded - cy.get("#masthead-logo").should("be.visible"); - // Only check for #app; ignores twitter and sidecar. - cy.checkA11y("#app", CYPRESS_ACCESSIBILITY_CONFIG); - }); }); diff --git a/yarn.lock b/yarn.lock index be5cb3c1a1..ec86094149 100644 --- a/yarn.lock +++ b/yarn.lock @@ -10740,9 +10740,9 @@ nanoclone@^0.2.1: integrity sha512-wynEP02LmIbLpcYw8uBKpcfF6dmg2vcpKqxeH5UcoKEYdExslsdUA4ugFauuaeYdTB76ez6gJW8XAZ6CgkXYxA== nanoid@^3.1.23: - version "3.3.1" - resolved "https://registry.yarnpkg.com/nanoid/-/nanoid-3.3.1.tgz#6347a18cac88af88f58af0b3594b723d5e99bb35" - integrity sha512-n6Vs/3KGyxPQd6uO0eH4Bv0ojGSUvuLlIHtC3Y0kEO23YRge8H9x1GCzLn28YX0H66pMkxuaeESFq4tKISKwdw== + version "3.3.8" + resolved "https://registry.yarnpkg.com/nanoid/-/nanoid-3.3.8.tgz#b1be3030bee36aaff18bacb375e5cce521684baf" + integrity sha512-WNLf5Sd8oZxOm+TzppcYk8gVOgP+l58xNy58D0nbUnOxOWRWvlcCV4kUF7ltmI6PsrLl/BgKEyS4mqsGChFN0w== nanomatch@^1.2.9: version "1.2.13"